
Physica D: Nonlinear Phenomena [SJR: 1.049] [HI: 102] [3 followers] Follow Hybrid journal (It can contain Open Access articles) ISSN (Print) 01672789 Published by Elsevier [3040 journals] 
 Finitetime thin film rupture driven by modified evaporative loss
 Authors: Hangjie Ji; Thomas P. Witelski
Pages: 1  15
Abstract: Publication date: 1 March 2017
Source:Physica D: Nonlinear Phenomena, Volume 342
Author(s): Hangjie Ji, Thomas P. Witelski
Rupture is a nonlinear instability resulting in a finitetime singularity as a film layer approaches zero thickness at a point. We study the dynamics of rupture in a generalized mathematical model of thin films of viscous fluids with modified evaporative effects. The governing lubrication model is a fourthorder nonlinear parabolic partial differential equation with a nonconservative loss term. Several different types of finitetime singularities are observed due to balances between conservative and nonconservative terms. Nonselfsimilar behavior and two classes of selfsimilar rupture solutions are analyzed and validated against high resolution PDE simulations.
PubDate: 20170114T04:47:15Z
DOI: 10.1016/j.physd.2016.10.002
Issue No: Vol. 342 (2017)
 Authors: Hangjie Ji; Thomas P. Witelski
 Stability on timedependent domains: convective and dilution effects
 Authors: R. Krechetnikov; E. Knobloch
Pages: 16  23
Abstract: Publication date: 1 March 2017
Source:Physica D: Nonlinear Phenomena, Volume 342
Author(s): R. Krechetnikov, E. Knobloch
We explore nearcritical behavior of spatially extended systems on timedependent spatial domains with convective and dilution effects due to domain flow. As a paradigm, we use the Swift–Hohenberg equation, which is the simplest nonlinear model with a nonzero critical wavenumber, to study dynamic pattern formation on timedependent domains. A universal amplitude equation governing weakly nonlinear evolution of patterns on timedependent domains is derived and proves to be a generalization of the standard Ginzburg–Landau equation. Its key solutions identified here demonstrate a substantial variety–spatially periodic states with a timedependent wavenumber, steady spatially nonperiodic states, and pulsetrain solutions–in contrast to extended systems on timefixed domains. The effects of domain flow, such as bifurcation delay due to domain growth and destabilization due to oscillatory domain flow, on the Eckhaus instability responsible for phase slips in spatially periodic states are analyzed with the help of both local and global stability analyses. A nonlinear phase equation describing the approach to a phaseslip event is derived. Detailed analysis of a phase slip using multiple time scale methods demonstrates different mechanisms governing the wavelength changing process at different stages.
PubDate: 20170114T04:47:15Z
DOI: 10.1016/j.physd.2016.10.003
Issue No: Vol. 342 (2017)
 Authors: R. Krechetnikov; E. Knobloch
 Full analysis of small hypercycles with shortcircuits in prebiotic
evolution Authors: Josep Sardanyés; J. Tomás Lázaro; Toni Guillamon; Ernest Fontich
Abstract: Publication date: Available online 5 January 2017
Source:Physica D: Nonlinear Phenomena
Author(s): Josep Sardanyés, J. Tomás Lázaro, Toni Guillamon, Ernest Fontich
It is known that hypercycles are sensitive to the socalled parasites and shortcircuits. While the impact of parasites has been widely investigated for wellmixed and spatial hypercycles, the effect of shortcircuits in hypercycles remains poorly understood. In this article we analyze the mean field and spatial dynamics of two small, asymmetric hypercycles with shortcircuits. Specifically, we analyze a twomember hypercycle where one of the species contains an autocatalytic loop, as the simplest hypercycle with a shortcircuit. Then, we extend this system by adding another species that closes a threemember hypercycle while keeping the autocatalytic shortcircuit and the twomember cycle. The mean field model allows us to discard the presence of stable or unstable periodic orbits for both systems. We characterize the bifurcations and transitions involved in the dominance of the shortcircuits i.e., in the reduction of the hypercycles’ size. The spatial simulations reveal a randomlike and mixed distribution of the replicators in the allspecies coexistence, ruling out the presence of largescale spatial patterns such as spirals or spots typical of larger, oscillating hypercycles. A MonteCarlo sampling of the parameter space for the wellmixed and the spatial models reveals that the probability of finding stable hypercycles with shortcircuits drastically diminishes from the twomember to the threemember system, especially at growing degradation rates of the replicators. These findings pose a big constrain in the increase of hypercycle’s size and complexity under the presence of inner cycles, suggesting the importance of a rapid growth of hypercycles able to generate spatial structures (e.g., rotating spirals) prior to the emergence of inner cycles. Our results can also be useful for the future design and implementation of synthetic cooperative systems containing catalytic shortcircuits.
PubDate: 20170114T04:47:15Z
DOI: 10.1016/j.physd.2016.12.004
 Authors: Josep Sardanyés; J. Tomás Lázaro; Toni Guillamon; Ernest Fontich
 A numerical estimate of the regularity of a family of Strange
Non–Chaotic Attractors Authors: Lluís Alsedà i Soler; Josep Maria Mondelo González; David Romero i Sànchez
Abstract: Publication date: Available online 5 January 2017
Source:Physica D: Nonlinear Phenomena
Author(s): Lluís Alsedà i Soler, Josep Maria Mondelo González, David Romero i Sànchez
We estimate numerically the regularities of a family of Strange Non–Chaotic Attractors related with one of the models studied in Grebogi et al. (1984) (see also Keller, 1996). To estimate these regularities we use wavelet analysis in the spirit of Llave and Petrov (2002) together with some adhoc techniques that we develop to overcome the theoretical difficulties that arise in the application of the method to the particular family that we consider. These difficulties are mainly due to the facts that we do not have an explicit formula for the attractor and it is discontinuous almost everywhere for some values of the parameters. Concretely we propose an algorithm based on the Fast Wavelet Transform. Also a quality check of the wavelet coefficients and regularity estimates is done.
PubDate: 20170114T04:47:15Z
DOI: 10.1016/j.physd.2016.12.006
 Authors: Lluís Alsedà i Soler; Josep Maria Mondelo González; David Romero i Sànchez
 Reducedspace Gaussian Process Regression for datadriven probabilistic
forecast of chaotic dynamical systems Authors: Zhong Yi Wan; Themistoklis P. Sapsis
Abstract: Publication date: Available online 5 January 2017
Source:Physica D: Nonlinear Phenomena
Author(s): Zhong Yi Wan, Themistoklis P. Sapsis
We formulate a reducedorder strategy for efficiently forecasting complex highdimensional dynamical systems entirely based on data streams. The first step of our method involves reconstructing the dynamics in a reducedorder subspace of choice using Gaussian Process Regression (GPR). GPR simultaneously allows for reconstruction of the vector field and more importantly, estimation of local uncertainty. The latter is due to (i) local interpolation error and (ii) truncation of the highdimensional phase space. This uncertainty component can be analytically quantified in terms of the GPR hyperparameters. In the second step we formulate stochastic models that explicitly take into account the reconstructed dynamics and their uncertainty. For regions of the attractor which are not sufficiently sampled for our GPR framework to be effective, an adaptive blended scheme is formulated to enforce correct statistical steady state properties, matching those of the real data. We examine the effectiveness of the proposed method to complex systems including the Lorenz 96, the KuramotoSivashinsky, as well as a prototype climate model. We also study the performance of the proposed approach as the intrinsic dimensionality of the system attractor increases in highly turbulent regimes.
PubDate: 20170114T04:47:15Z
DOI: 10.1016/j.physd.2016.12.005
 Authors: Zhong Yi Wan; Themistoklis P. Sapsis
 Spiral disk packings
 Authors: Yoshikazu Yamagishi; Takamichi Sushida
Abstract: Publication date: Available online 26 December 2016
Source:Physica D: Nonlinear Phenomena
Author(s): Yoshikazu Yamagishi, Takamichi Sushida
It is shown that van Iterson’s metric for disk packings, proposed in 1907 in the study of a centric model of spiral phyllotaxis, defines a bounded distance function in the plane. This metric is also related to the bifurcation of Voronoi tilings for logarithmic spiral lattices, through the continued fraction expansion of the divergence angle. The phase diagrams of disk packings and Voronoi tilings for logarithmic spirals are dual graphs to each other. This gives a rigorous proof that van Iterson’s diagram in the centric model is connected and simply connected. It is a nonlinear analog of the duality between the phase diagrams for disk packings and Voronoi tilings on the linear lattices, having the modular group symmetry.
PubDate: 20170105T04:02:55Z
DOI: 10.1016/j.physd.2016.12.003
 Authors: Yoshikazu Yamagishi; Takamichi Sushida
 Cascades of alternating pitchfork and flip bifurcations in Hbridge
inverters Authors: Viktor Avrutin; Zhanybai T. Zhusubaliyev; Erik Mosekilde
Abstract: Publication date: Available online 28 December 2016
Source:Physica D: Nonlinear Phenomena
Author(s): Viktor Avrutin, Zhanybai T. Zhusubaliyev, Erik Mosekilde
Power electronic DC/AC converters (inverters) play an important role in modern power engineering. These systems are also of considerable theoretical interest because their dynamics is influenced by the presence of two vastly different forcing frequencies. As a consequence, inverter systems may be modeled in terms of piecewise smooth maps with an extremely high number of switching manifolds. We have recently shown that models of this type can demonstrate a complicated bifurcation structure associated with the occurrence of border collisions. Considering the example of a PWM Hbridge singlephase inverter, the present paper discusses a number of unusual phenomena that can occur in piecewise smooth maps with a very large number of switching manifolds. We show in particular how smooth (pitchfork and flip) bifurcations may form a macroscopic pattern that stretches across the overall bifurcation structure. We explain the observed bifurcation phenomena, show under which conditions they occur, and describe them quantitatively by means of an analytic approximation.
PubDate: 20170105T04:02:55Z
DOI: 10.1016/j.physd.2016.12.008
 Authors: Viktor Avrutin; Zhanybai T. Zhusubaliyev; Erik Mosekilde
 Classical quasisteady state reduction—A mathematical
characterization Authors: Alexandra Goeke; Sebastian Walcher; Eva Zerz
Abstract: Publication date: Available online 30 December 2016
Source:Physica D: Nonlinear Phenomena
Author(s): Alexandra Goeke, Sebastian Walcher, Eva Zerz
We discuss parameter dependent polynomial ordinary differential equations that model chemical reaction networks. By classical quasisteady state (QSS) reduction we understand the following familiar (heuristically motivated) mathematical procedure: Set the rate of change for certain (a priori chosen) variables equal to zero and use the resulting algebraic equations to obtain a system of smaller dimension for the remaining variables. This procedure will generally be valid only for certain parameter ranges. We start by showing that the reduction is accurate if and only if the corresponding parameter is what we call a QSS parameter value, and that the reduction is approximately accurate if and only if the corresponding parameter is close to a QSS parameter value. The QSS parameter values can be characterized by polynomial equations and inequations, hence parameter ranges for which QSS reduction is valid are accessible in an algorithmic manner. A defining characteristic of a QSS parameter value is that the algebraic variety defined by the QSS relations is invariant for the differential equation. A closer investigation of the associated systems shows the existence of further invariant sets; here singular perturbations enter the picture in a natural manner. We compare QSS reduction and singular perturbation reduction, and show that, while they do not agree in general, they do, up to lowest order in a small parameter, for a quite large and relevant class of examples. This observation, in turn, allows the computation of QSS reductions even in cases where an explicit resolution of the polynomial equations is not possible.
PubDate: 20170105T04:02:55Z
DOI: 10.1016/j.physd.2016.12.002
 Authors: Alexandra Goeke; Sebastian Walcher; Eva Zerz
 Characterizing complex networks through statistics of Möbius
transformations Authors: Vladimir Jaćimović; Aladin Crnkić
Abstract: Publication date: Available online 31 December 2016
Source:Physica D: Nonlinear Phenomena
Author(s): Vladimir Jaćimović, Aladin Crnkić
It is wellknown now that dynamics of large populations of globally (alltoall) coupled oscillators can be reduced to lowdimensional submanifolds (WS transformation and OA ansatz). Marvel et al. (2009) described an intriguing algebraic structure standing behind this reduction: oscillators evolve by the action of the group of Möbius transformations. Of course, dynamics in complex networks of coupled oscillators is highly complex and not reducible. Still, closer look unveils that even in complex networks some (possibly overlapping) groups of oscillators evolve by Möbius transformations. In this paper we study properties of the network by identifying Möbius transformations in the dynamics of oscillators. This enables us to introduce some new (statistical) concepts that characterize the network. In particular, the notion of coherence of the network (or subnetwork) is proposed. This conceptual approach is meaningful for the broad class of networks, including those with timedelayed, noisy or mixed interactions. In this paper several simple (random) graphs are studied illustrating the meaning of the concepts introduced in the paper.
PubDate: 20170105T04:02:55Z
DOI: 10.1016/j.physd.2016.12.007
 Authors: Vladimir Jaćimović; Aladin Crnkić
 Complicated quasiperiodic oscillations and chaos from driven
piecewiseconstant circuit: Chenciner bubbles do not necessarily occur via
simple phaselocking Authors: Tri Quoc Truong; Tadashi Tsubone; Munehisa Sekikawa; Naohiko Inaba
Pages: 1  9
Abstract: Publication date: 15 February 2017
Source:Physica D: Nonlinear Phenomena, Volume 341
Author(s): Tri Quoc Truong, Tadashi Tsubone, Munehisa Sekikawa, Naohiko Inaba
We analyze the complex quasiperiodic oscillations and chaos generated by two coupled piecewiseconstant hysteresis oscillators driven by a rectangular wave force. Oscillations generate Arnol’d resonance webs wherein lower dimensional resonance tongues extend such as that of a web in numerous directions. We provide the fundamental tools for bifurcation analysis of nonautonomous piecewiseconstant oscillators. To optimize the outstanding simplicity of piecewiseconstant circuits, we formulate a generalized procedure for calculating the Lyapunov exponents in nonautonomous piecewiseconstant dynamics. The Lyapunov exponents in these dynamics can be calculated with a precision approximately similar to that of maps. We observe twoparameter Lyapunov diagrams near the fundamental resonance region called Chenciner bubbles, wherein the oscillation frequencies of the two oscillators and the force are synchronized with a ratio of 1:1:1. Inevitably, the hysteresis considerably distorts the Chenciner bubbles. This result suggests that the Chenciner bubbles do not necessarily occur due to simple phaselocking of twodimensional tori that can be explained by homeomorphism on the circle. Furthermore, we observe the Farey sequence in the experimental measurements.
PubDate: 20161226T03:35:57Z
DOI: 10.1016/j.physd.2016.09.008
Issue No: Vol. 341 (2016)
 Authors: Tri Quoc Truong; Tadashi Tsubone; Munehisa Sekikawa; Naohiko Inaba
 Gaussian noise and the twonetwork frustrated Kuramoto model
 Authors: Andrew B. Holder; Mathew L. Zuparic; Alexander C. Kalloniatis
Pages: 10  32
Abstract: Publication date: 15 February 2017
Source:Physica D: Nonlinear Phenomena, Volume 341
Author(s): Andrew B. Holder, Mathew L. Zuparic, Alexander C. Kalloniatis
We examine analytically and numerically a variant of the stochastic Kuramoto model for phase oscillators coupled on a general network. Two populations of phased oscillators are considered, labelled ‘Blue’ and ‘Red’, each with their respective networks, internal and external couplings, natural frequencies, and frustration parameters in the dynamical interactions of the phases. We disentangle the different ways that additive Gaussian noise may influence the dynamics by applying it separately on zero modes or normal modes corresponding to a Laplacian decomposition for the subgraphs for Blue and Red. Under the linearisation ansatz that the oscillators of each respective network remain relatively phasesynchronised centroids or clusters, we are able to obtain simple closedform expressions using the Fokker–Planck approach for the dynamics of the average angle of the two centroids. In some cases, this leads to subtle effects of metastability that we may analytically describe using the theory of ratchet potentials. These considerations are extended to a regime where one of the populations has fragmented in two. The analytic expressions we derive largely predict the dynamics of the nonlinear system seen in numerical simulation. In particular, we find that noise acting on a more tightly coupled population allows for improved synchronisation of the other population where deterministically it is fragmented.
PubDate: 20161226T03:35:57Z
DOI: 10.1016/j.physd.2016.09.009
Issue No: Vol. 341 (2016)
 Authors: Andrew B. Holder; Mathew L. Zuparic; Alexander C. Kalloniatis
 Microorganism billiards
 Authors: Saverio E. Spagnolie; Colin Wahl; Joseph Lukasik; JeanLuc Thiffeault
Pages: 33  44
Abstract: Publication date: 15 February 2017
Source:Physica D: Nonlinear Phenomena, Volume 341
Author(s): Saverio E. Spagnolie, Colin Wahl, Joseph Lukasik, JeanLuc Thiffeault
Recent experiments and numerical simulations have shown that certain types of microorganisms “reflect” off of a flat surface at a critical angle of departure, independent of the angle of incidence. The nature of the reflection may be active (cell and flagellar contact with the surface) or passive (hydrodynamic) interactions. We explore the billiardlike motion of a body with this empirical reflection law inside a regular polygon and show that the dynamics can settle on a stable periodic orbit or can be chaotic, depending on the swimmer’s departure angle and the domain geometry. The dynamics are often found to be robust to the introduction of weak random fluctuations. The Lyapunov exponent of swimmer trajectories can be positive or negative, can have extremal values, and can have discontinuities depending on the degree of the polygon. A passive sorting device is proposed that traps swimmers of different departure angles into separate bins. We also study the external problem of a microorganism swimming in a patterned environment of square obstacles, where the departure angle dictates the possibility of trapping or diffusive trajectories.
PubDate: 20161226T03:35:57Z
DOI: 10.1016/j.physd.2016.09.010
Issue No: Vol. 341 (2016)
 Authors: Saverio E. Spagnolie; Colin Wahl; Joseph Lukasik; JeanLuc Thiffeault
 A theory of synchrony for active compartments with delays coupled through
bulk diffusion Authors: Bin Xu; Paul C. Bressloff
Pages: 45  59
Abstract: Publication date: 15 February 2017
Source:Physica D: Nonlinear Phenomena, Volume 341
Author(s): Bin Xu, Paul C. Bressloff
We extend recent work on the analysis of synchronization in a pair of biochemical oscillators coupled by linear bulk diffusion, in order to explore the effects of discrete delays. More specifically, we consider two wellmixed, identical compartments located at either end of a bounded, onedimensional domain. The compartments can exchange signaling molecules with the bulk domain, within which the signaling molecules undergo diffusion. The concentration of signaling molecules in each compartment is modeled by a delay differential equation (DDE), while the concentration in the bulk medium is modeled by a partial differential equation (PDE) for diffusion. Coupling in the resulting PDE–DDE system is via flux terms at the boundaries. Using linear stability analysis, numerical simulations and bifurcation analysis, we investigate the effect of diffusion on the onset of a supercritical Hopf bifurcation. The direction of the Hopf bifurcation is determined by numerical simulations and a winding number argument. Near a Hopf bifurcation point, we find that there are oscillations with two possible modes: inphase and antiphase. Moreover, the critical delay for oscillations to occur increases with the diffusion coefficient. Our numerical results suggest that the selection of the inphase or antiphase oscillation is sensitive to the diffusion coefficient, time delay and coupling strength. For slow diffusion and weak coupling both modes can coexist, while for fast diffusion and strong coupling, only one of the modes is dominant, depending on the explicit choice of DDE.
PubDate: 20161226T03:35:57Z
DOI: 10.1016/j.physd.2016.10.001
Issue No: Vol. 341 (2016)
 Authors: Bin Xu; Paul C. Bressloff
 A theory of synchrony by coupling through a diffusive chemical signal
 Authors: Jia Gou; WeiYin Chiang; PikYin Lai; Michael J. Ward; YueXian Li
Pages: 1  17
Abstract: Publication date: 15 January 2017
Source:Physica D: Nonlinear Phenomena, Volume 339
Author(s): Jia Gou, WeiYin Chiang, PikYin Lai, Michael J. Ward, YueXian Li
We formulate and analyze oscillatory dynamics associated with a model of dynamically active, but spatially segregated, compartments that are coupled through a chemical signal that diffuses in the bulk medium between the compartments. The coupling between each compartment and the bulk is due to both feedback terms to the compartmental dynamics and flux boundary conditions at the interface between the compartment and the bulk. Our coupled model consists of dynamically active compartments located at the two ends of a 1D bulk region of spatial extent 2 L . The dynamics in the two compartments is modeled by Sel’kov kinetics, and the signaling molecule between the twocompartments is assumed to undergo both diffusion, with diffusivity D , and firstorder, linear, bulk degradation. For the resulting PDE–ODE system, we construct a symmetric steadystate solution and analyze the stability of this solution to either inphase synchronous or antiphase synchronous perturbations about the midline x = L . The conditions for the onset of oscillatory dynamics, as obtained from a linearization of the steadystate solution, are studied using a winding number approach. Global branches of either inphase or antiphase periodic solutions, and their associated stability properties, are determined numerically. For the case of a linear coupling between the compartments and the bulk, with coupling strength β , a phase diagram, in the parameter space D versus β is constructed that shows the existence of a rather wide parameter regime where stable inphase synchronized oscillations can occur between the two compartments. By using a Floquetbased approach, this analysis with linear coupling is then extended to determine Hopf bifurcation thresholds for a periodic chain of evenlyspaced dynamically active units. Finally, we consider one particular case of a nonlinear coupling between two active compartments and the bulk. It is shown that stable inphase and antiphase synchronous oscillations also occur in certain parameter regimes, but as isolated solution branches that are disconnected from the steadystate solution branch.
PubDate: 20161127T16:42:30Z
DOI: 10.1016/j.physd.2016.08.004
Issue No: Vol. 339 (2016)
 Authors: Jia Gou; WeiYin Chiang; PikYin Lai; Michael J. Ward; YueXian Li
 Global dynamics for steep nonlinearities in two dimensions
 Authors: Tomáš Gedeon; Shaun Harker; Hiroshi Kokubu; Konstantin Mischaikow; Hiroe Oka
Pages: 18  38
Abstract: Publication date: 15 January 2017
Source:Physica D: Nonlinear Phenomena, Volume 339
Author(s): Tomáš Gedeon, Shaun Harker, Hiroshi Kokubu, Konstantin Mischaikow, Hiroe Oka
This paper discusses a novel approach to obtaining mathematically rigorous results on the global dynamics of ordinary differential equations. We study switching models of regulatory networks. To each switching network we associate a Morse graph, a computable object that describes a Morse decomposition of the dynamics. In this paper we show that all smooth perturbations of the switching system share the same Morse graph and we compute explicit bounds on the size of the allowable perturbation. This shows that computationally tractable switching systems can be used to characterize dynamics of smooth systems with steep nonlinearities.
PubDate: 20161127T16:42:30Z
DOI: 10.1016/j.physd.2016.08.006
Issue No: Vol. 339 (2016)
 Authors: Tomáš Gedeon; Shaun Harker; Hiroshi Kokubu; Konstantin Mischaikow; Hiroe Oka
 Analysis of the Poisson–Nernst–Planck equation in a ball for modeling
the Voltage–Current relation in neurobiological microdomains Authors: J. Cartailler; Z. Schuss; D. Holcman
Pages: 39  48
Abstract: Publication date: 15 January 2017
Source:Physica D: Nonlinear Phenomena, Volume 339
Author(s): J. Cartailler, Z. Schuss, D. Holcman
The electrodiffusion of ions is often described by the Poisson–Nernst–Planck (PNP) equations, which couple nonlinearly the charge concentration and the electric potential. This model is used, among others, to describe the motion of ions in neuronal microcompartments. It remains at this time an open question how to determine the relaxation and the steady state distribution of voltage when an initial charge of ions is injected into a domain bounded by an impermeable dielectric membrane. The purpose of this paper is to construct an asymptotic approximation to the solution of the stationary PNP equations in a d dimensional ball ( d = 1 , 2 , 3 ) in the limit of large total charge. In this geometry the PNP system reduces to the Liouville–Gelfand–Bratú (LGB) equation, with the difference that the boundary condition is Neumann, not Dirichlet, and there is a minus sign in the exponent of the exponential term. The entire boundary is impermeable to ions and the electric field satisfies the compatibility condition of Poisson’s equation. These differences replace attraction by repulsion in the LGB equation, thus completely changing the solution. We find that the voltage is maximal in the center and decreases toward the boundary. We also find that the potential drop between the center and the surface increases logarithmically in the total number of charges and not linearly, as in classical capacitance theory. This logarithmic singularity is obtained for d = 3 from an asymptotic argument and cannot be derived from the analysis of the phase portrait. These results are used to derive the relation between the outward current and the voltage in a dendritic spine, which is idealized as a dielectric sphere connected smoothly to the nerve axon by a narrow neck. This is a fundamental microdomain involved in neuronal communication. We compute the escape rate of an ion from the steady density in a ball, which models a neuronal spine head, to a small absorbing window in the sphere. We predict that the current is defined by the narrow neck that is connected to the sphere by a small absorbing window, as suggested by the narrow escape theory, while voltage is controlled by the PNP equations independently of the neck.
PubDate: 20161127T16:42:30Z
DOI: 10.1016/j.physd.2016.09.001
Issue No: Vol. 339 (2016)
 Authors: J. Cartailler; Z. Schuss; D. Holcman
 Numerical analysis of the rescaling method for parabolic problems with
blowup in finite time Authors: V.T. Nguyen
Pages: 49  65
Abstract: Publication date: 15 January 2017
Source:Physica D: Nonlinear Phenomena, Volume 339
Author(s): V.T. Nguyen
In this work, we study the numerical solution for parabolic equations whose solutions have a common property of blowing up in finite time and the equations are invariant under the following scaling transformation u ↦ u λ ( x , t ) : = λ 2 p − 1 u ( λ x , λ 2 t ) . For that purpose, we apply the rescaling method proposed by Berger and Kohn (1988) to such problems. The convergence of the method is proved under some regularity assumption. Some numerical experiments are given to derive the blowup profile verifying henceforth the theoretical results.
PubDate: 20161127T16:42:30Z
DOI: 10.1016/j.physd.2016.09.002
Issue No: Vol. 339 (2016)
 Authors: V.T. Nguyen
 A Hierarchical Bayes Ensemble Kalman Filter
 Authors: Michael Tsyrulnikov; Alexander Rakitko
Pages: 1  16
Abstract: Publication date: 1 January 2017
Source:Physica D: Nonlinear Phenomena, Volume 338
Author(s): Michael Tsyrulnikov, Alexander Rakitko
A new ensemble filter that allows for the uncertainty in the prior distribution is proposed and tested. The filter relies on the conditional Gaussian distribution of the state given the modelerror and predictabilityerror covariance matrices. The latter are treated as random matrices and updated in a hierarchical Bayes scheme along with the state. The (hyper)prior distribution of the covariance matrices is assumed to be inverse Wishart. The new Hierarchical Bayes Ensemble Filter (HBEF) assimilates ensemble members as generalized observations and allows ordinary observations to influence the covariances. The actual probability distribution of the ensemble members is allowed to be different from the true one. An approximation that leads to a practicable analysis algorithm is proposed. The new filter is studied in numerical experiments with a doubly stochastic onevariable model of “truth”. The model permits the assessment of the variance of the truth and the true filtering error variance at each time instance. The HBEF is shown to outperform the EnKF and the HEnKF by Myrseth and Omre (2010) in a wide range of filtering regimes in terms of performance of its primary and secondary filters.
PubDate: 20161120T14:57:33Z
DOI: 10.1016/j.physd.2016.07.009
Issue No: Vol. 338 (2016)
 Authors: Michael Tsyrulnikov; Alexander Rakitko
 The tennis racket effect in a threedimensional rigid body
 Authors: Léo Van Damme; Pavao Mardešić; Dominique Sugny
Pages: 17  25
Abstract: Publication date: 1 January 2017
Source:Physica D: Nonlinear Phenomena, Volume 338
Author(s): Léo Van Damme, Pavao Mardešić, Dominique Sugny
We propose a complete theoretical description of the tennis racket effect, which occurs in the free rotation of a threedimensional rigid body. This effect is characterized by a flip ( π  rotation) of the head of the racket when a full ( 2 π ) rotation around the unstable inertia axis is considered. We describe the asymptotics of the phenomenon and conclude about the robustness of this effect with respect to the values of the moments of inertia and the initial conditions of the dynamics. This shows the generality of this geometric property which can be found in a variety of rigid bodies. A simple analytical formula is derived to estimate the twisting effect in the general case. Different examples are discussed.
PubDate: 20161120T14:57:33Z
DOI: 10.1016/j.physd.2016.07.010
Issue No: Vol. 338 (2016)
 Authors: Léo Van Damme; Pavao Mardešić; Dominique Sugny
 Stability analysis of amplitude death in delaycoupled highdimensional
map networks and their design procedure Authors: Tomohiko Watanabe; Yoshiki Sugitani; Keiji Konishi; Naoyuki Hara
Pages: 26  33
Abstract: Publication date: 1 January 2017
Source:Physica D: Nonlinear Phenomena, Volume 338
Author(s): Tomohiko Watanabe, Yoshiki Sugitani, Keiji Konishi, Naoyuki Hara
The present paper studies amplitude death in highdimensional maps coupled by timedelay connections. A linear stability analysis provides several sufficient conditions for an amplitude death state to be unstable, i.e., an odd number property and its extended properties. Furthermore, necessary conditions for stability are provided. These conditions, which reduce trialanderror tasks for design, and the convex direction, which is a popular concept in the field of robust control, allow us to propose a design procedure for system parameters, such as coupling strength, connection delay, and input–output matrices, for a given network topology. These analytical results are confirmed numerically using delayed logistic maps, generalized Henon maps, and piecewise linear maps.
PubDate: 20161120T14:57:33Z
DOI: 10.1016/j.physd.2016.07.011
Issue No: Vol. 338 (2016)
 Authors: Tomohiko Watanabe; Yoshiki Sugitani; Keiji Konishi; Naoyuki Hara
 Generalized uncertainty principle and analogue of quantum gravity in
optics Authors: Maria Chiara Braidotti; Ziad H. Musslimani; Claudio Conti
Pages: 34  41
Abstract: Publication date: 1 January 2017
Source:Physica D: Nonlinear Phenomena, Volume 338
Author(s): Maria Chiara Braidotti, Ziad H. Musslimani, Claudio Conti
The design of optical systems capable of processing and manipulating ultrashort pulses and ultrafocused beams is highly challenging with far reaching fundamental technological applications. One key obstacle routinely encountered while implementing subwavelength optical schemes is how to overcome the limitations set by standard Fourier optics. A strategy to overcome these difficulties is to utilize the concept of a generalized uncertainty principle (GUP) which has been originally developed to study quantum gravity. In this paper we propose to use the concept of GUP within the framework of optics to show that the generalized Schrödinger equation describing short pulses and ultrafocused beams predicts the existence of a minimal spatial or temporal scale which in turn implies the existence of maximally localized states. Using a Gaussian wavepacket with complex phase, we derive the corresponding generalized uncertainty relation and its maximally localized states. Furthermore, we numerically show that the presence of nonlinearity helps the system to reach its maximal localization. Our results may trigger further theoretical and experimental tests for practical applications and analogues of fundamental physical theories.
PubDate: 20161120T14:57:33Z
DOI: 10.1016/j.physd.2016.08.001
Issue No: Vol. 338 (2016)
 Authors: Maria Chiara Braidotti; Ziad H. Musslimani; Claudio Conti
 Initial–boundary layer associated with the nonlinear
Darcy–Brinkman–Oberbeck–Boussinesq system Authors: Mingwen Fei; Daozhi Han; Xiaoming Wang
Pages: 42  56
Abstract: Publication date: 1 January 2017
Source:Physica D: Nonlinear Phenomena, Volume 338
Author(s): Mingwen Fei, Daozhi Han, Xiaoming Wang
In this paper, we study the vanishing Darcy number limit of the nonlinear Darcy–Brinkman–Oberbeck–Boussinesq system (DBOB). This singular perturbation problem involves singular structures both in time and in space giving rise to initial layers, boundary layers and initial–boundary layers. We construct an approximate solution to the DBOB system by the method of multiple scale expansions. The convergence with optimal convergence rates in certain Sobolev norms is established rigorously via the energy method.
PubDate: 20161120T14:57:33Z
DOI: 10.1016/j.physd.2016.08.002
Issue No: Vol. 338 (2016)
 Authors: Mingwen Fei; Daozhi Han; Xiaoming Wang
 Twodimensional localized structures in harmonically forced oscillatory
systems Authors: Y.P. Ma; E. Knobloch
Pages: 1  17
Abstract: Publication date: 15 December 2016
Source:Physica D: Nonlinear Phenomena, Volume 337
Author(s): Y.P. Ma, E. Knobloch
Twodimensional spatially localized structures in the complex Ginzburg–Landau equation with 1:1 resonance are studied near the simultaneous presence of a steady front between two spatially homogeneous equilibria and a supercritical Turing bifurcation on one of them. The bifurcation structures of steady circular fronts and localized target patterns are computed in the Turingstable and Turingunstable regimes. In particular, localized target patterns grow along the solution branch via ring insertion at the core in a process reminiscent of defectmediated snaking in one spatial dimension. Stability of axisymmetric solutions on these branches with respect to axisymmetric and nonaxisymmetric perturbations is determined, and parameter regimes with stable axisymmetric oscillons are identified. Direct numerical simulations reveal novel depinning dynamics of localized target patterns in the radial direction, and of circular and planar localized hexagonal patterns in the fully twodimensional system.
PubDate: 20161030T22:02:28Z
DOI: 10.1016/j.physd.2016.07.003
Issue No: Vol. 337 (2016)
 Authors: Y.P. Ma; E. Knobloch
 A comparison of macroscopic models describing the collective response of
sedimenting rodlike particles in shear flows Authors: Christiane Helzel; Athanasios E. Tzavaras
Pages: 18  29
Abstract: Publication date: 15 December 2016
Source:Physica D: Nonlinear Phenomena, Volume 337
Author(s): Christiane Helzel, Athanasios E. Tzavaras
We consider a kinetic model, which describes the sedimentation of rodlike particles in dilute suspensions under the influence of gravity, presented in Helzel and Tzavaras (submitted for publication). Here we restrict our considerations to shear flow and consider a simplified situation, where the particle orientation is restricted to the plane spanned by the direction of shear and the direction of gravity. For this simplified kinetic model we carry out a linear stability analysis and we derive two different nonlinear macroscopic models which describe the formation of clusters of higher particle density. One of these macroscopic models is based on a diffusive scaling, the other one is based on a socalled quasidynamic approximation. Numerical computations, which compare the predictions of the macroscopic models with the kinetic model, complete our presentation.
PubDate: 20161030T22:02:28Z
DOI: 10.1016/j.physd.2016.07.004
Issue No: Vol. 337 (2016)
 Authors: Christiane Helzel; Athanasios E. Tzavaras
 Exploiting stiffness nonlinearities to improve flow energy capture from
the wake of a bluff body Authors: Ali H. Alhadidi; Hamid Abderrahmane; Mohammed F. Daqaq
Pages: 30  42
Abstract: Publication date: 15 December 2016
Source:Physica D: Nonlinear Phenomena, Volume 337
Author(s): Ali H. Alhadidi, Hamid Abderrahmane, Mohammed F. Daqaq
Fluid–structure coupling mechanisms such as wake galloping have been recently utilized to develop scalable flow energy harvesters. Unlike traditional rotarytype generators which are known to suffer serious scalability issues because their efficiency drops significantly as their size decreases; wakegalloping flow energy harvesters (FEHs) operate using a very simple motion mechanism, and, hence can be scaled down to fit the desired application. Nevertheless, wakegalloping FEHs have their own shortcomings. Typically, a wakegalloping FEH has a linear restoring force which results in a very narrow lockin region. As a result, it does not perform well under the broad range of shedding frequencies normally associated with a variable flow speed. To overcome this critical problem, this article demonstrates theoretically and experimentally that, a bistable restoring force can be used to broaden the steadystate bandwidth of wake galloping FEHs and, thereby to decrease their sensitivity to variations in the flow speed. An experimental case study is carried out in a wind tunnel to compare the performance of a bistable and a linear FEH under single and multifrequency vortex street. An experimentallyvalidated lumpedparameters model of the bistable harvester is also introduced, and solved using the method of multiple scales to study the influence of the shape of the potential energy function on the output voltage.
PubDate: 20161030T22:02:28Z
DOI: 10.1016/j.physd.2016.07.005
Issue No: Vol. 337 (2016)
 Authors: Ali H. Alhadidi; Hamid Abderrahmane; Mohammed F. Daqaq
 Variety of strange pseudohyperbolic attractors in threedimensional
generalized Hénon maps Authors: A.S. Gonchenko; S.V. Gonchenko
Pages: 43  57
Abstract: Publication date: 15 December 2016
Source:Physica D: Nonlinear Phenomena, Volume 337
Author(s): A.S. Gonchenko, S.V. Gonchenko
In the present paper we focus on the problem of the existence of strange pseudohyperbolic attractors for threedimensional diffeomorphisms. Such attractors are genuine strange attractors in that sense that each orbit in the attractor has positive maximal Lyapunov exponent and this property is robust, i.e., it holds for all close systems. We restrict attention to the study of pseudohyperbolic attractors that contain only one fixed point. Then we show that threedimensional maps may have only 5 different types of such attractors, which we call the discrete Lorenz, figure8, doublefigure8, superfigure8, and superLorenz attractors. We find the first four types of attractors in threedimensional generalized Hénon maps of form x ̄ = y , y ̄ = z , z ̄ = B x + A z + C y + g ( y , z ) , where A , B and C are parameters ( B is the Jacobian) and g ( 0 , 0 ) = g ′ ( 0 , 0 ) = 0 .
PubDate: 20161030T22:02:28Z
DOI: 10.1016/j.physd.2016.07.006
Issue No: Vol. 337 (2016)
 Authors: A.S. Gonchenko; S.V. Gonchenko
 Oscillatory instabilities of gap solitons in a repulsive
Bose–Einstein condensate Authors: P.P. Kizin; D.A. Zezyulin; G.L. Alfimov
Pages: 58  66
Abstract: Publication date: 15 December 2016
Source:Physica D: Nonlinear Phenomena, Volume 337
Author(s): P.P. Kizin, D.A. Zezyulin, G.L. Alfimov
The paper is devoted to numerical study of stability of nonlinear localized modes (“gap solitons”) for the spatially onedimensional Gross–Pitaevskii equation (1D GPE) with periodic potential and repulsive interparticle interactions. We use the Evans function approach combined with the exterior algebra formulation in order to detect and describe weak oscillatory instabilities. We show that the simplest (“fundamental”) gap solitons in the first and in the second spectral gap undergo oscillatory instabilities for certain values of the frequency parameter (i.e., the chemical potential). The number of unstable eigenvalues and the associated instability rates are described. Several stable and unstable more complex (nonfundamental) gap solitons are also discussed. The results obtained from the Evans function approach are independently confirmed using the direct numerical integration of the GPE.
PubDate: 20161030T22:02:28Z
DOI: 10.1016/j.physd.2016.07.007
Issue No: Vol. 337 (2016)
 Authors: P.P. Kizin; D.A. Zezyulin; G.L. Alfimov
 Limit cycles in planar piecewise linear differential systems with
nonregular separation line Authors: Pedro Toniol Cardin; Joan Torregrosa
Pages: 67  82
Abstract: Publication date: 15 December 2016
Source:Physica D: Nonlinear Phenomena, Volume 337
Author(s): Pedro Toniol Cardin, Joan Torregrosa
In this paper we deal with planar piecewise linear differential systems defined in two zones. We consider the case when the two linear zones are angular sectors of angles α and 2 π − α , respectively, for α ∈ ( 0 , π ) . We study the problem of determining lower bounds for the number of isolated periodic orbits in such systems using Melnikov functions. These limit cycles appear studying higher order piecewise linear perturbations of a linear center. It is proved that the maximum number of limit cycles that can appear up to a sixth order perturbation is five. Moreover, for these values of α , we prove the existence of systems with four limit cycles up to fifth order and, for α = π / 2 , we provide an explicit example with five up to sixth order. In general, the nonregular separation line increases the number of periodic orbits in comparison with the case where the two zones are separated by a straight line.
PubDate: 20161030T22:02:28Z
DOI: 10.1016/j.physd.2016.07.008
Issue No: Vol. 337 (2016)
 Authors: Pedro Toniol Cardin; Joan Torregrosa
 Causal hydrodynamics from kinetic theory by doublet scheme in
renormalizationgroup method Authors: Kyosuke Tsumura; Yuta Kikuchi; Teiji Kunihiro
Pages: 1  27
Abstract: Publication date: 1 December 2016
Source:Physica D: Nonlinear Phenomena, Volume 336
Author(s): Kyosuke Tsumura, Yuta Kikuchi, Teiji Kunihiro
We develop a general framework in the renormalizationgroup (RG) method for extracting a mesoscopic dynamics from an evolution equation by incorporating some excited (fast) modes as additional components to the invariant manifold spanned by zero modes. We call this framework the doublet scheme. The validity of the doublet scheme is first tested and demonstrated by taking the Lorenz model as a simple threedimensional dynamical system; it is shown that the twodimensional reduced dynamics on the attractive manifold composed of the wouldbe zero and a fast modes are successfully obtained in a natural way. We then apply the doublet scheme to construct causal hydrodynamics as a mesoscopic dynamics of kinetic theory, i.e., the Boltzmann equation, in a systematic manner with no adhoc assumption. It is found that our equation has the same form as Grad’s thirteenmoment causal hydrodynamic equation, but the microscopic formulae of the transport coefficients and relaxation times are different. In fact, in contrast to the Grad equation, our equation leads to the same expressions for the transport coefficients as given by the Chapman–Enskog expansion method and suggests novel formulae of the relaxation times expressed in terms of relaxation functions which allow a natural physical interpretation of the relaxation times. Furthermore, our theory nicely gives the explicit forms of the distribution function and the thirteen hydrodynamic variables in terms of the linearized collision operator, which in turn clearly suggest the proper ansatz forms of them to be adopted in the method of moments.
PubDate: 20161016T12:47:09Z
DOI: 10.1016/j.physd.2016.06.012
Issue No: Vol. 336 (2016)
 Authors: Kyosuke Tsumura; Yuta Kikuchi; Teiji Kunihiro
 Towards the modeling of nanoindentation of virus shells: Do substrate
adhesion and geometry matter? Authors: Arthur Bousquet; Bogdan Dragnea; Manel Tayachi; Roger Temam
Pages: 28  38
Abstract: Publication date: 1 December 2016
Source:Physica D: Nonlinear Phenomena, Volume 336
Author(s): Arthur Bousquet, Bogdan Dragnea, Manel Tayachi, Roger Temam
Soft nanoparticles adsorbing at surfaces undergo deformation and buildup of elastic strain as a consequence of interfacial adhesion of similar magnitude with constitutive interactions. An example is the adsorption of virus particles at surfaces, a phenomenon of central importance for experiments in virus nanoindentation and for understanding of virus entry. The influence of adhesion forces and substrate corrugation on the mechanical response to indentation has not been studied. This is somewhat surprising considering that many singlestranded RNA icosahedral viruses are organized by soft intermolecular interactions while relatively strong adhesion forces are required for virus immobilization for nanoindentation. This article presents numerical simulations via finite elements discretization investigating the deformation of a thick shell in the context of slow evolution linear elasticity and in presence of adhesion interactions with the substrate. We study the influence of the adhesion forces in the deformation of the virus model under axial compression on a flat substrate by comparing the force–displacement curves for a shell having elastic constants relevant to virus capsids with and without adhesion forces derived from the LennardJones potential. Finally, we study the influence of the geometry of the substrate in twodimensions by comparing deformation of the virus model adsorbed at the cusp between two cylinders with that on a flat surface.
PubDate: 20161016T12:47:09Z
DOI: 10.1016/j.physd.2016.06.013
Issue No: Vol. 336 (2016)
 Authors: Arthur Bousquet; Bogdan Dragnea; Manel Tayachi; Roger Temam
 Fluctuations induced transition of localization of granular objects caused
by degrees of crowding Authors: Soutaro Oda; Yoshitsugu Kubo; ChwenYang Shew; Kenichi Yoshikawa
Pages: 39  46
Abstract: Publication date: 1 December 2016
Source:Physica D: Nonlinear Phenomena, Volume 336
Author(s): Soutaro Oda, Yoshitsugu Kubo, ChwenYang Shew, Kenichi Yoshikawa
Fluctuations are ubiquitous in both microscopic and macroscopic systems, and an investigation of confined particles under fluctuations is relevant to how living cells on the earth maintain their lives. Inspired by biological cells, we conduct the experiment through a very simple fluctuating system containing one or several large spherical granular particles and multiple smaller ones confined on a cylindrical dish under vertical vibration. We find a universal behavior that large particles preferentially locate in cavity interior due to the fact that large particles are depleted from the cavity wall by small spheres under vertical vibration in the actual experiment. This universal behavior can be understood from the standpoint of entropy.
PubDate: 20161016T12:47:09Z
DOI: 10.1016/j.physd.2016.06.014
Issue No: Vol. 336 (2016)
 Authors: Soutaro Oda; Yoshitsugu Kubo; ChwenYang Shew; Kenichi Yoshikawa
 Coupled oscillators on evolving networks
 Authors: R.K. Singh; Trilochan Bagarti
Pages: 47  52
Abstract: Publication date: 1 December 2016
Source:Physica D: Nonlinear Phenomena, Volume 336
Author(s): R.K. Singh, Trilochan Bagarti
In this work we study coupled oscillators on evolving networks. We find that the steady state behavior of the system is governed by the relative values of the spread in natural frequencies and the global coupling strength. For coupling strong in comparison to the spread in frequencies, the system of oscillators synchronize and when coupling strength and spread in frequencies are large, a phenomenon similar to amplitude death is observed. The network evolution provides a mechanism to build interoscillator connections and once a dynamic equilibrium is achieved, oscillators evolve according to their local interactions. We also find that the steady state properties change by the presence of additional time scales. We demonstrate these results based on numerical calculations studying dynamical evolution of limitcycle and van der Pol oscillators.
PubDate: 20161016T12:47:09Z
DOI: 10.1016/j.physd.2016.06.015
Issue No: Vol. 336 (2016)
 Authors: R.K. Singh; Trilochan Bagarti
 On Wright’s generalized Bessel kernel
 Authors: Lun Zhang
Pages: 92  119
Abstract: Publication date: 1 February 2017
Source:Physica D: Nonlinear Phenomena, Volume 340
Author(s): Lun Zhang
In this paper, we consider the Wright’s generalized Bessel kernel K ( α , θ ) ( x , y ) defined by θ x α ∫ 0 1 J α + 1 θ , 1 θ ( u x ) J α + 1 , θ ( ( u y ) θ ) u α d u , α > − 1 , θ > 0 , where J a , b ( x ) = ∑ j = 0 ∞ ( − x ) j j ! Γ ( a + b j ) , a ∈ C , b > − 1 , is Wright’s generalization of the Bessel function. This nonsymmetric kernel, which generalizes the classical Bessel kernel (corresponding to θ = 1 ) in random matrix theory, is the hard edge scaling limit of the correlation kernel for certain Muttalib–Borodin ensembles. We show that, if θ is rational, i.e., θ = m n with m , n ∈ N , g c d ( m , n ) = 1 , and α > m − 1 − m n , the Wright’s generalized Bessel kernel is integrable in the sense of Its–Izergin–Korepin–Slavnov. We then come to the Fredholm determinant of this kernel over the union of several scaled intervals, which can also be interpreted as the gap probability (the probability of finding no particles) on these intervals. The integrable structure allows us to obtain a system of coupled partial differential equations associated with the corresponding Fredholm determinant as well as a Hamiltonian interpretation. As a consequence, we are able to represent the gap probability over a single interval ( 0 , s ) in terms of a solution of a system of nonlinear ordinary differential equations.
PubDate: 20161218T03:09:08Z
DOI: 10.1016/j.jat.2016.09.002
Issue No: Vol. 213 (2016)
 Authors: Lun Zhang
 Windows of opportunity for synchronization in stochastically coupled maps
 Authors: Olga Golovneva; Russell Jeter Igor Belykh Maurizio Porfiri
Abstract: Publication date: 1 February 2017
Source:Physica D: Nonlinear Phenomena, Volume 340
Author(s): Olga Golovneva, Russell Jeter, Igor Belykh, Maurizio Porfiri
Several complex systems across science and engineering display on–off intermittent coupling among their units. Most of the current understanding of synchronization in switching networks relies on the fast switching hypothesis, where the network dynamics evolves at a much faster time scale than the individual units. Recent numerical evidence has demonstrated the existence of windows of opportunity, where synchronization may be induced through nonfast switching. Here, we study synchronization of coupled maps whose coupling gains stochastically switch with an arbitrary switching period. We determine the role of the switching period on synchronization through a detailed analytical treatment of the Lyapunov exponent of the stochastic dynamics. Through closedform expressions and numerical findings, we demonstrate the emergence of windows of opportunity and elucidate their nontrivial relationship with the stability of synchronization under static coupling. Our results are expected to provide a rigorous basis for understanding the dynamic mechanisms underlying the emergence of windows of opportunity and leverage nonfast switching in the design of evolving networks.
Graphical abstract
PubDate: 20161218T03:09:08Z
 Authors: Olga Golovneva; Russell Jeter Igor Belykh Maurizio Porfiri
 Arnold tongues in a billiard problem in nonlinear and nonequilibrium
systems Authors: Tomoyuki Miyaji
Abstract: Publication date: 1 February 2017
Source:Physica D: Nonlinear Phenomena, Volume 340
Author(s): Tomoyuki Miyaji
We study a billiard problem in nonlinear and nonequilibrium systems. This is motivated by the motions of a traveling spot in a reaction–diffusion system (RDS) in a rectangular domain. We consider a fourdimensional dynamical system, defined by ordinary differential equations. This was first derived by S.I. Ei et al. (2006), based on a reduced system on the center manifold in a neighborhood of a pitchfork bifurcation of a stationary spot for the RDS. In contrast to the classical billiard problem, this defines a dynamical system that is dissipative rather than conservative, and has an attractor. According to previous numerical studies, the attractor of the system changes depending on parameters such as the aspect ratio of the domain. It may be periodic, quasiperiodic, or chaotic. In this paper, we elucidate that it results from parameters crossing Arnold tongues and that the organizing center is a Hopf–Hopf bifurcation of the trivial equilibrium.
PubDate: 20161218T03:09:08Z
 Authors: Tomoyuki Miyaji
 Corrigendum to “Dynamics and stability of a discrete breather in a
harmonically excited chain with vibroimpact onsite potential” [Physica
D 292–293 (2015) 8–28] Authors: Nathan Perchikov; O.V. Gendelman
Abstract: Publication date: 1 February 2017
Source:Physica D: Nonlinear Phenomena, Volume 340
Author(s): Nathan Perchikov, O.V. Gendelman
PubDate: 20161218T03:09:08Z
 Authors: Nathan Perchikov; O.V. Gendelman
 Databased stochastic model reduction for the Kuramoto–Sivashinsky
equation Authors: Fei Kevin; Lin Alexandre Chorin
Abstract: Publication date: 1 February 2017
Source:Physica D: Nonlinear Phenomena, Volume 340
Author(s): Fei Lu, Kevin K. Lin, Alexandre J. Chorin
The problem of constructing databased, predictive, reduced models for the Kuramoto–Sivashinsky equation is considered, under circumstances where one has observation data only for a small subset of the dynamical variables. Accurate prediction is achieved by developing a discretetime stochastic reduced system, based on a NARMAX (Nonlinear Autoregressive Moving Average with eXogenous input) representation. The practical issue, with the NARMAX representation as with any other, is to identify an efficient structure, i.e., one with a small number of terms and coefficients. This is accomplished here by estimating coefficients for an approximate inertial form. The broader significance of the results is discussed.
PubDate: 20161218T03:09:08Z
 Authors: Fei Kevin; Lin Alexandre Chorin
 Timing variation in an analytically solvable chaotic system
 Authors: J.N. Blakely; M.S. Milosavljevic N.J. Corron
Abstract: Publication date: 1 February 2017
Source:Physica D: Nonlinear Phenomena, Volume 340
Author(s): J.N. Blakely, M.S. Milosavljevic, N.J. Corron
We present analytic solutions for a chaotic dynamical system that do not have the regular timing characteristic of recently reported solvable chaotic systems. The dynamical system can be viewed as a first order filter with binary feedback. The feedback state may be switched only at instants defined by an external clock signal. Generalizing from a period one clock, we show analytic solutions for period two and higher period clocks. We show that even when the clock ‘ticks’ randomly the chaotic system has an analytic solution. These solutions can be visualized in a stroboscopic map whose complexity increases with the complexity of the clock. We provide both analytic results as well as experimental data from an electronic circuit implementation of the system. Our findings bridge the gap between the irregular timing of well known chaotic systems such as Lorenz and Rossler and the well regulated oscillations of recently reported solvable chaotic systems.
Graphical abstract
PubDate: 20161218T03:09:08Z
 Authors: J.N. Blakely; M.S. Milosavljevic N.J. Corron
 Elastic and inelastic collisions of swarms
 Authors: Dieter Armbruster; Stephan Martin; Andrea Thatcher
Abstract: Publication date: Available online 8 December 2016
Source:Physica D: Nonlinear Phenomena
Author(s): Dieter Armbruster, Stephan Martin, Andrea Thatcher
Scattering interactions of swarms in potentials that are generated by an attraction–repulsion model are studied. In free space, swarms in this model form a welldefined steady state describing the translation of a stable formation of the particles whose shape depends on the interaction potential. Thus, the collision between a swarm and a boundary or between two swarms can be treated as (quasi)particle scattering. Such scattering experiments result in internal excitations of the swarm or in bound states, respectively. In addition, varying a parameter linked to the relative importance of damping and potential forces drives transitions between elastic and inelastic scattering of the particles. By tracking the swarm’s center of mass, a refraction rule is derived via simulations relating the incoming and outgoing directions of a swarm hitting the wall. Iterating the map derived from the refraction law allows us to predict and understand the dynamics and bifurcations of swarms in square boxes and in channels.
PubDate: 20161211T02:34:16Z
DOI: 10.1016/j.physd.2016.11.008
 Authors: Dieter Armbruster; Stephan Martin; Andrea Thatcher
 Numerical bifurcation for the capillary Whitham equation
 Authors: Filippo Remonato; Henrik Kalisch
Abstract: Publication date: Available online 6 December 2016
Source:Physica D: Nonlinear Phenomena
Author(s): Filippo Remonato, Henrik Kalisch
The socalled Whitham equation arises in the modeling of free surface water waves, and combines a generic nonlinear quadratic term with the exact linear dispersion relation for gravity waves on the free surface of a fluid with finite depth. In this work, the effect of incorporating capillarity into the Whitham equation is in focus. The capillary Whitham equation is a nonlocal equation similar to the usual Whitham equation, but containing an additional term with a coefficient depending on the Bond number which measures the relative strength of capillary and gravity effects on the wave motion. A spectral collocation scheme for computing approximations to periodic traveling waves for the capillary Whitham equation is put forward. Numerical approximations of periodic traveling waves are computed using a bifurcation approach, and a number of bifurcation curves are found. Our analysis uncovers a rich structure of bifurcation patterns, including subharmonic bifurcations, as well as connecting and crossing branches. Indeed, for some values of the Bond number, the bifurcation diagram features distinct branches of solutions which intersect at a secondary bifurcation point. The same branches may also cross without connecting, and some bifurcation curves feature selfcrossings without selfconnections.
PubDate: 20161211T02:34:16Z
DOI: 10.1016/j.physd.2016.11.003
 Authors: Filippo Remonato; Henrik Kalisch
 Selfassembly of a filament by curvatureinducing proteins
 Authors: James Kwiecinski; S. Jonathan Chapman; Alain Goriely
Abstract: Publication date: Available online 10 December 2016
Source:Physica D: Nonlinear Phenomena
Author(s): James Kwiecinski, S. Jonathan Chapman, Alain Goriely
We explore a simplified macroscopic model of membrane shaping by means of curvaturesensing BAR proteins. Equations describing the interplay between the shape of a freely floating filament in a fluid and the adhesion kinetics of proteins are derived from mechanical principles. The constant curvature solutions that arise from this system are studied using weakly nonlinear analysis. We show that the stability of the filament’s shape is completely characterized by the parameters associated with protein recruitment and establish that in the bistable regime, proteins aggregate on the filament forming regions of high and low curvature. This pattern formation is then followed by phasecoarsening that resolves on a timescale dependent on protein diffusion and drift across the filament, which contend to smooth and maintain the pattern respectively. The model is generalized for multiple species of BAR proteins and we show that the stability of the assembled shape is determined by a competition between proteins attaching on opposing sides.
PubDate: 20161211T02:34:16Z
DOI: 10.1016/j.physd.2016.12.001
 Authors: James Kwiecinski; S. Jonathan Chapman; Alain Goriely
 Swarming in bounded domains
 Authors: Dieter Armbruster; Sébastien Motsch; Andrea Thatcher
Abstract: Publication date: Available online 9 December 2016
Source:Physica D: Nonlinear Phenomena
Author(s): Dieter Armbruster, Sébastien Motsch, Andrea Thatcher
The Vicsek model is a prototype for the emergence of collective motion. In free space, it is characterized by a swarm of particles all moving in the same direction. Since this dynamic does not include attraction among particles, the swarm, while aligning in velocity space, has no spatial coherence. Adding specular reflection at the boundaries generates global spatial coherence of the swarms while maintaining its velocity alignment. We investigate numerically how the geometry of the domain influences the Vicsek model using three type of geometry: a channel, a disk and a rectangle. Varying the parameters of the Vicsek model (e.g. noise levels and influence horizons), we discuss the mechanisms that generate spatial coherence and show how they create new dynamical solutions of the swarming motions in these geometries. Several observables are introduced to characterize the simulated patterns (e.g. mass profile, center of mass, connectivity of the swarm).
PubDate: 20161211T02:34:16Z
DOI: 10.1016/j.physd.2016.11.009
 Authors: Dieter Armbruster; Sébastien Motsch; Andrea Thatcher
 Excitability, mixedmode oscillations and transition to chaos in a
stochastic ice ages model Authors: D.V. Alexandrov; I.A. Bashkirtseva; L.B. Ryashko
Abstract: Publication date: Available online 30 November 2016
Source:Physica D: Nonlinear Phenomena
Author(s): D.V. Alexandrov, I.A. Bashkirtseva, L.B. Ryashko
Motivated by an important geophysical significance, we consider the influence of stochastic forcing on a simple threedimensional climate model previously derived by Saltzman and Sutera. A nonlinear dynamical system governing three physical variables, the bulk ocean temperature, continental and marine ice masses, is analyzed in deterministic and stochastic cases. It is shown that the attractor of deterministic model is either a stable equilibrium or a limit cycle. We demonstrate that the process of continental ice melting occurs with a noisedependent time delay as compared with marine ice melting. The paleoclimate cyclicity which is near 100 ky in a wide range of model parameters abruptly increases in the vicinity of a bifurcation point and depends on the noise intensity. In a zone of stable equilibria, the 3D climate model under consideration is extremely excitable. Even for a weak random noise, the stochastic trajectories demonstrate a transition from small to largeamplitude stochastic oscillations (SLASO). In a zone of stable cycles, SLASO transitions are analyzed too. We show that such stochastic transitions play an important role in the formation of a mixedmode paleoclimate scenario. This mixedmode dynamics with the intermittency of large and smallamplitude stochastic oscillations and coherence resonance are investigated via analysis of interspike intervals. A tendency of dynamic paleoclimate to abrupt and rapid glaciations and deglaciations as well as its transition from order to chaos with increasing noise are shown.
PubDate: 20161204T02:03:09Z
DOI: 10.1016/j.physd.2016.11.007
 Authors: D.V. Alexandrov; I.A. Bashkirtseva; L.B. Ryashko
 One and twodimensional bright solitons in inhomogeneous defocusing
nonlinearities with an antisymmetric periodic gain and loss Authors: Dengchu Guo; Jing Xiao; Linlin Gu; Hongzhen Jin; Liangwei Dong
Abstract: Publication date: Available online 2 December 2016
Source:Physica D: Nonlinear Phenomena
Author(s): Dengchu Guo, Jing Xiao, Linlin Gu, Hongzhen Jin, Liangwei Dong
We address that various branches of bright solitons exist in a spatially inhomogeneous defocusing nonlinearity with an imprinted antisymmetric periodic gainloss profile. The spectra of such systems with a purely imaginary potential never become complex and thus the paritytime symmetry is unbreakable. The mergence between pairs of soliton branches occurs at a critical gainloss strength, above which no soliton solutions can be found. Intriguingly, which pair of soliton branches will merge together can be changed by varying the modulation frequency of gain and loss. Most branches of onedimensional solitons are stable in wide parameter regions. We also provide the first example of twodimensional bright solitons with unbreakable paritytime symmetry.
PubDate: 20161204T02:03:09Z
DOI: 10.1016/j.physd.2016.11.005
 Authors: Dengchu Guo; Jing Xiao; Linlin Gu; Hongzhen Jin; Liangwei Dong
 A nonperturbative analytic expression of signal amplification factor in
stochastic resonance Authors: Asish Kumar Dhara
Abstract: Publication date: Available online 21 November 2016
Source:Physica D: Nonlinear Phenomena
Author(s): Asish Kumar Dhara
We put forward a nonperturbative scheme to calculate the response of an overdamped bistable system driven by a Gaussian white noise and perturbed by a weak monochromatic force (signal) analytically. The formalism takes into account infinite number of perturbation terms of a perturbation series with amplitude of the signal as an expansion parameter. The contributions of infinite number of relaxation modes of the stochastic dynamics to the response are also taken into account in this formalism. A closed form analytic expression of the response is obtained. Only the knowledge of the first nontrivial eigenvalue and the lowest eigenfunction of the unperturbed Fokker–Planck operator are needed to evaluate the response. The response calculated from the derived analytic expression matches fairly well with the numerical results.
PubDate: 20161127T16:42:30Z
DOI: 10.1016/j.physd.2016.11.002
 Authors: Asish Kumar Dhara
 Optical dispersive shock waves in defocusing colloidal media
 Authors: X. An; T.R. Marchant; N.F. Smyth
Abstract: Publication date: Available online 24 November 2016
Source:Physica D: Nonlinear Phenomena
Author(s): X. An, T.R. Marchant, N.F. Smyth
The propagation of an optical dispersive shock wave, generated from a jump discontinuity in light intensity, in a defocussing colloidal medium is analysed. The equations governing nonlinear light propagation in a colloidal medium consist of a nonlinear Schrödinger equation for the beam and an algebraic equation for the medium response. In the limit of low light intensity, these equations reduce to a perturbed higher order nonlinear Schrödinger equation. Solutions for the leading and trailing edges of the colloidal dispersive shock wave are found using modulation theory. This is done for both the perturbed nonlinear Schrödinger equation and the full colloid equations for arbitrary light intensity. These results are compared with numerical solutions of the colloid equations.
PubDate: 20161127T16:42:30Z
DOI: 10.1016/j.physd.2016.11.004
 Authors: X. An; T.R. Marchant; N.F. Smyth
 Lowdimensional reducedorder models for statistical response and
uncertainty quantification: Barotropic turbulence with topography Authors: Di Qi; Andrew J. Majda
Abstract: Publication date: Available online 25 November 2016
Source:Physica D: Nonlinear Phenomena
Author(s): Di Qi, Andrew J. Majda
A lowdimensional reducedorder statistical closure model is developed for quantifying the uncertainty to changes in forcing in a barotropic turbulent system with topography involving interactions between smallscale motions and a largescale mean flow. Imperfect model sensitivity is improved through a recent mathematical strategy for calibrating model errors in a training phase, where information theory and linear statistical response theory are combined in a systematic fashion to achieve the optimal model parameters. Statistical theories about a Gaussian invariant measure and the exact statistical energy equations are also developed for the truncated barotropic equations that can be used to improve the imperfect model prediction skill. A stringent paradigm model of 57 degrees of freedom is used to display the feasibility of the reducedorder methods. This simple model creates largescale zonal mean flow shifting directions from westward to eastward jets with an abrupt change in amplitude when perturbations are applied, and prototype blocked and unblocked patterns can be generated in this simple model similar to the real natural system. Principal statistical responses in mean and variance can be captured by the reducedorder models with desirable accuracy and efficiency with only 3 resolved modes. An even more challenging regime with nonGaussian equilibrium statistics using the fluctuation equations is also tested in the reducedorder models with accurate prediction using the first 5 resolved modes. These reducedorder models also show potential for uncertainty quantification and prediction in more complex realistic geophysical turbulent dynamical systems.
PubDate: 20161127T16:42:30Z
DOI: 10.1016/j.physd.2016.11.006
 Authors: Di Qi; Andrew J. Majda
 Macroscopic heat transport equations and heat waves in nonequilibrium
states Authors: Yangyu Guo; David Jou; Moran Wang
Abstract: Publication date: Available online 16 November 2016
Source:Physica D: Nonlinear Phenomena
Author(s): Yangyu Guo, David Jou, Moran Wang
Heat transport may behave as wave propagation when the time scale of processes decreases to be comparable to or smaller than the relaxation time of heat carriers. In this work, a generalized heat transport equation including nonlinear, nonlocal and relaxation terms is proposed, which sums up the CattaneoVernotte, dualphaselag and phonon hydrodynamic models as special cases. In the frame of this equation, the heat wave propagations are investigated systematically in nonequilibrium steady states, which were usually studied around equilibrium states. The phase (or front) speed of heat waves is obtained through a perturbation solution to the heat differential equation, and found to be intimately related to the nonlinear and nonlocal terms. Thus, potential heat wave experiments in nonequilibrium states are devised to measure the coefficients in the generalized equation, which may throw light on understanding the physical mechanisms and macroscopic modeling of nanoscale heat transport.
PubDate: 20161120T14:57:33Z
DOI: 10.1016/j.physd.2016.10.005
 Authors: Yangyu Guo; David Jou; Moran Wang
 Spatiotemporal control to eliminate cardiac alternans using isostable
reduction Authors: Dan Wilson; Jeff Moehlis
Abstract: Publication date: Available online 16 November 2016
Source:Physica D: Nonlinear Phenomena
Author(s): Dan Wilson, Jeff Moehlis
Cardiac alternans, an arrhythmia characterized by a beattobeat alternation of cardiac action potential durations, is widely believed to facilitate the transition from normal cardiac function to ventricular fibrillation and sudden cardiac death. Alternans arises due to an instability of a healthy period1 rhythm, and most dynamical control strategies either require extensive knowledge of the cardiac system, making experimental validation difficult, or are model independent and sacrifice important information about the specific system under study. Isostable reduction provides an alternative approach, in which the response of a system to external perturbations can be used to reduce the complexity of a cardiac system, making it easier to work with from an analytical perspective while retaining many of its important features. Here, we use isostable reduction strategies to reduce the complexity of partial differential equation models of cardiac systems in order to develop energy optimal strategies for the elimination of alternans. Resulting control strategies require significantly less energy to terminate alternans than comparable strategies and do not require continuous state feedback.
PubDate: 20161120T14:57:33Z
DOI: 10.1016/j.physd.2016.11.001
 Authors: Dan Wilson; Jeff Moehlis
 Modulational instability in a PTsymmetric vector nonlinear
Schrödinger system Authors: J.T. Cole; K.G. Makris Z.H. Musslimani D.N. Christodoulides Rotter
Abstract: Publication date: 1 December 2016
Source:Physica D: Nonlinear Phenomena, Volume 336
Author(s): J.T. Cole, K.G. Makris, Z.H. Musslimani, D.N. Christodoulides, S. Rotter
A class of exact multicomponent constant intensity solutions to a vector nonlinear Schrödinger (NLS) system in the presence of an external P T symmetric complex potential is constructed. This type of uniform wave pattern displays a nontrivial phase whose spatial dependence is induced by the lattice structure. In this regard, light can propagate without scattering while retaining its original form despite the presence of inhomogeneous gain and loss. These constantintensity continuous waves are then used to perform a modulational instability analysis in the presence of both nonhermitian media and cubic nonlinearity. A linear stability eigenvalue problem is formulated that governs the dynamical evolution of the periodic perturbation and its spectrum is numerically determined using Fourier–Floquet–Bloch theory. In the selffocusing case, we identify an intensity threshold above which the constantintensity modes are modulationally unstable for any Floquet–Bloch momentum belonging to the first Brillouin zone. The picture in the selfdefocusing case is different. Contrary to the bulk vector case, where instability develops only when the waves are strongly coupled, here an instability occurs in the strong and weak coupling regimes. The linear stability results are supplemented with direct (nonlinear) numerical simulations.
PubDate: 20161016T12:47:09Z
 Authors: J.T. Cole; K.G. Makris Z.H. Musslimani D.N. Christodoulides Rotter